boxavg(1)                   General Commands Manual                  boxavg(1)

       boxavg - averages images from specified locations in an image file

       boxavg  [options]  image_input_file  model_input_file  average_out-

       Boxavg will average images at points specified in an IMOD model file.
       By default, it take all points from open contour and scattered point
       objects, but specific objects can be selected instead.  After computing
       an average, it can then align each extracted image with the average by
       searching for the shift that minimizes the standard deviation of the
       difference between the two.

       Boxavg uses the PIP package for input exclusively (see the manual page
       for pip).  The following options can be specified either as command
       line arguments (with the -) or one per line in a command file or param-
       eter file (without the -).  Options can be abbreviated to unique let-
       ters; the currently valid abbreviations for short names are shown in

       -image (-i) OR -InputImageFile      File name
              Input file with images containing features to average.  If this
              option is not entered, the first non-option argument will be
              used for this input file.

       -points (-po) OR -PointModelFile    File name
              Name of model file with points to be averaged.  If this option
              is not entered, the second non-option argument will be used for
              this input file.

       -output (-ou) OR -OutputFile   File name
              Output file for average image.  If this option is not entered,
              the third non-option argument will be used for this output file.

       -piece (-pi) OR -PieceListFile      File name
              Name of piece list file if image is montaged or out of sequence

       -objects (-ob) OR -ObjectsToAverage      List of integer ranges
              List of objects with points to average (comma-separated ranges
              allowed).  The default is to take all points from all open con-
              tour or scattered point objects.  This option can be used to
              select a subset of objects in the model or force the use of a
              closed contour object.

       -box (-b) OR -BoxSizeXandY     Two integers
              Size of box to average in X and Y

       -mode (-m) OR -ModeOfOutput    Integer
              Mode for output: 0 for byte, 1 for integer, 2 for real, 6 for
              unsigned integer.  The default is the same as that of the input.

       -passes (-pas) OR -PassesThroughData     Integer
              Number of passes through the data, either 1 or 2.  On the second
              pass, the boxes will be aligned to the average from the first
              pass.  The default is 2; enter 1 to skip the alignment pass.

       -linear (-l) OR -LinearInterpolation
              Use linear instead of cubic interpolation when extracting box

         These options are not needed when Xcorrstack is used to correlate
         an average with images.

       -size (-si) OR -SizeOfOutputXandY   Two integers
              Size of output file in X and Y (default is same size as box)

       -fill (-f) OR -FillValue       Floating point
              Value to fill with when output array is bigger than box.  The
              default is the mean along the edge of the average image.  This
              entry is ignored if the output is the same size as the box.

       -split (-sp) OR -SplitIntoCorners
              Split average into the four corners of the output array

       -zero (-z) OR -ZeroMean
              Shift the output to have a zero mean value.  This option is
              ignored if the data mode of the output is bytes or unsigned

       -param (-par) OR -ParameterFile     Parameter file
              Read parameter entries as keyword-value pairs from a parameter

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard input.

       Written by David Mastronarde, 4/26/89
       Converted to PIP, using a model file and non-integer coordinates,

       Email bug reports to mast at colorado dot edu.

IMOD                                4.10.22                          boxavg(1)